On Sat, May 04, 2013, Angelica Parente wrote:
>
> I've been very frustratingly trying to run MMPBSA on ligands...
> I've tried looking at the trajectories (~34000 frames, 64ns)...
> Error: gb>0 is incompatible with periodic boundary conditions.
> Running MMPBSA.MPI on 24 processors
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> PrmtopError: Couldn't predict mask from topology files!
> Your ligand residues must be sequential in your complex.
I just want to make sure that you are taking seriously the instructions in the
manual that you know how to run mm-pbsa calculations "by hand" (to understand
in detail what is going on) before using the automated scripts (see the first
two paragraphs of the MMPBSA.py chapter).
In your case, try a simple calculation with 100 frames, and choose GB as a
solvation model. Study carefully what is happening, making sure that you know
how to create the needed prmtop files, how various components add up to the
total, and so on.
Then you can gradually add frames, consider different ligands, try some simple
options with PB instead of GB, and so on. Don't do any parallel calculations
at this stage.
As a final step, to get better statistics, you can consider increasing the
number of frames, seeing if various subsets of the trajectory give consistent
results, and so on.
...good luck....dac
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Received on Sat May 04 2013 - 10:00:02 PDT
